Bonnie Hurwitz is seated next to the most pivotal piece of equipment in her lab, her computer, a window into the world of microbes such as bacteria, archaea and viruses. She says viruses are her favorite microbe of all.
"And when I say viruses, I mean phages. Phages are viruses that infect bacteria. One of my first loves is viral ecology and understanding how viruses interact with and reprogram their bacterial hosts," says Hurwitz, assistant professor of biosystems engineering at the University of Arizona.
But to understand these viruses is a complex matter. Very little is known about them. So scientists need to begin identifying and classifying them to learn how they interact with their fellow microbes in specific environments. To do that, researchers must first sequence the virus’ DNA and then make sense of it both scientifically and systematically.
And that’s where Hurwitz and her computer come into play. Hurwitz is a computational biologist.
"I build and use bioinformatics tools for understanding the molecular biology and cross talk between the microbes in our bodies or our environment," she says.
Hurwitz and her collaborators at Protocols.io decided to create a virtual community network known as VERVE Net, or the Viral Ecology Research Virtual Exchange Network. The network will bring together researchers whose goal is to better understand individual communities of viruses, known as viromes. Hurwitz received $700,000 in funding last spring from the Gordon and Betty Moore Foundation to launch the project.
VERVE Net will be hosted by the computational infrastructure of the UA's iPlant Collaborative, building on the foundation created when Hurwitz developed iMicrobe in collaboration with the creators of iPlant (and also hosted by iPlant). Thus, iPlant is ideally positioned to provide data management for VERVE Net, and to serve as a collaboration platform for researchers to communicate about shared datasets.
VERVE Net includes several innovative features, all of which facilitate collaboration and learning. For example, researchers can share their laboratory protocols with other researchers; they can copy other labs’ protocols for use in their own labs and modify them as they see fit; and they can discuss these protocols with others as questions or issues arise.
"We’re trying to make sure protocols and analyses for molecular biology and for bioinformatics are accessible," Hurwitz says. "Once they are, researchers can then guide each other on how to best use these protocols in different environments. For example, one protocol may work well for samples from high saline environments, like seawater, but not in other environments, and a researcher may not become aware of that until they talk with someone else."
Traditionally, scientists often don’t have ready access to other scientists’ laboratory protocols unless they seek them out. Even then, effectively using other labs’ protocols may be problematic. Viruses are especially difficult to work with given their sheer numbers, genetic variability and dearth of DNA.
"Viruses are always mutating," Hurwitz says. "This means that no single gene exists to track viruses in their environments like in bacteria. Instead, viral ecologists must sequence the entire genetic content of a viral community given very low quantities of DNA, and there’s a whole lot of hocus-pocus involved in sequencing it."
What’s more, Hurwitz says, the whole concept of classifying genes and species in viruses is not well defined.
"When you do an environmental sampling — say, in the ocean — and you compare all of the sequences to the known protein universe, only about seven percent of the sequences match anything," she says. "So the vast majority of our data, more than 90 percent, is completely unknown. We’re finding and discovering new viruses that we have never seen before and know nothing about. On top of that, a different suite of tools are needed for analyzing viruses where very few reference genomes exist."
That’s why VERVE Net also will include portals for online discussions, research developments, researcher profiles and upcoming conferences.
"The viral ecology community in and of itself is relatively small," Hurwitz says. "This is about getting interconnected. People can share their data, they can share their tools, their thoughts, their publications and their ideas, and it all comes together in this one place.
"The field is changing very rapidly. We’re inventing stuff as we go, and that’s why this community forum is essential."